Source: murasaki Version: 1.68.6-10 X-Debbugs-CC: debian-ci@lists.debian.org Severity: serious User: debian-ci@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of murasaki the autopkgtest of murasaki fails in testing when that autopkgtest is run with the binary packages of murasaki from unstable. It passes when run with only packages from testing and on all other architectures that we test for. In tabular form: pass fail murasaki from testing 1.68.6-10 on armhf all others from testing from testing I copied some of the output at the bottom of this report. Currently this regression is blocking the migration to testing [1]. Can you please investigate the situation and fix it? More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=murasaki https://ci.debian.net/data/autopkgtest/testing/armhf/m/murasaki/8582325/log.gz autopkgtest [19:57:51]: test run-unit-test: [----------------------- Test Murasaki on NZ_GG705055.fna Created output directory: /tmp/autopkgtest-lxc.razmgtoz/downtmp/autopkgtest_tmp/output Verbosity level is: 0 Writing to: output/test Pattern is: 101 Max usable hash bits: 27 Hit filter is: 0 Hash table type is: EcoHash Hashing every: 1 base Histogram detail is: 0 Hashing function is: 3 Collision profiling is: disabled Repeats are: unmasked Mergefilter is at: 100 Random seed: 1606939072 (automatic) Bitscore output: on Leave status records: no Join neighbors is: off Target memory is: 3.12 GB Retain members is: true Store repeatmap? yes Reverse complement data is generated on the fly Rifts allowed: 0 Fuzzy Extension: yes Score by minimum pair: yes Gapped anchors: no Large sequence support is: enabled => seqpos is 4 bytes Murasaki version 1.68.6 (LARGESEQ) Loading NZ_GG705055.fna Read 398859bp (389.51 KBp) in 0.035 seconds (11.0 MBp/s) Done with forward strand (410644bp). Preparing reverse complement... <-> Reversing metdata. Done. Seq NZ_GG705055.fna loaded. 401.02 KB Loading NZ_GG705055.gbk Read 398859bp (389.51 KBp) in 0.048 seconds (7.9 MBp/s) Done with forward strand (410644bp). Preparing reverse complement... <-> Reversing metdata. Done. Seq NZ_GG705055.gbk loaded. 401.02 KB Sequence loading took: 0.083 seconds Forward frequencies: A:28.0367% C:23.1004% G:20.9036% T:27.9593% Global base frequencies: A/T:55.996% C/G:44.004% Pat: 3 bases long with weight 2 1 101 Computing hash parameters... Using 4 hashbits 0%......... (T -0.170 seconds) ETA: Wed Dec 2 19:57:52 2020 10%......... (T -0.152 seconds) ETA: Wed Dec 2 19:57:52 2020 20%......... (T -0.133 seconds) ETA: Wed Dec 2 19:57:52 2020 30%......... (T -0.114 seconds) ETA: Wed Dec 2 19:57:52 2020 40%......... (T -0.095 seconds) ETA: Wed Dec 2 19:57:52 2020 50%......... (T -0.076 seconds) ETA: Wed Dec 2 19:57:52 2020 60%......... (T -0.057 seconds) ETA: Wed Dec 2 19:57:52 2020 70%......... (T -0.038 seconds) ETA: Wed Dec 2 19:57:52 2020 80%......... (T -0.017 seconds) ETA: Wed Dec 2 19:57:52 2020 91%........ Acceptable hash function found after 1000 cycles. Best uses 2/2 bases and has 0 empties from 2 inputs. Score: 0.925992 (cf. worst: -4.54276) Entropy: high: 1 lo: 1 total: 2 bases (mean: 1 stddev: 0) Total correlation penalty: 0 Post cleanup: w[0]>>13 ^ w[0]>>14 {2} 10 == w[ 0]>>13: -.C w[ 0]>>14: A.- Ecolist (optimistic): (seqbits: 2 idxbits: 20 minBlocks: 1 initblocks: 1) Ecolist (optimistic): Expcted entries per list: 17 Ecolist (optimistic): Minimum chunks per list: 1 Would take minimum 128.000000 bytes to make perfect hash. Hashing 1.52 MB of sequence requires: ~ linear (in seq length) hashing cost of 4.18 MB ~ linear (in seq length) expected anchor cost of 18.80 MB Initial hash table uses: 128 bytes (4 bits, 16 entries) Expected memory usage (without anchors): 4.18 MB Expected memory usage (with anchors): 22.98 MB Hash parameters computed in 0.187 seconds Creating storage structures: 16 entries in 128 bytes space. Storage structures created in: 0.000 seconds Hashing NZ_GG705055.fna forwards 0%......... (T -0.050 seconds) ETA: Wed Dec 2 19:57:52 2020 10%......... (T -0.047 seconds) ETA: Wed Dec 2 19:57:52 2020 20%......... (T -0.043 seconds) ETA: Wed Dec 2 19:57:52 2020 30%......... (T -0.037 seconds) ETA: Wed Dec 2 19:57:52 2020 40%......... (T -0.031 seconds) ETA: Wed Dec 2 19:57:52 2020 50%......... (T -0.025 seconds) ETA: Wed Dec 2 19:57:52 2020 60%......... (T -0.019 seconds) ETA: Wed Dec 2 19:57:52 2020 70%......... (T -0.013 seconds) ETA: Wed Dec 2 19:57:52 2020 80%......... (T -0.006 seconds) ETA: Wed Dec 2 19:57:52 2020 90%......... Hashing NZ_GG705055.fna backwards 0%......... (T -0.058 seconds) ETA: Wed Dec 2 19:57:52 2020 10%......... (T -0.052 seconds) ETA: Wed Dec 2 19:57:52 2020 20%......... (T -0.047 seconds) ETA: Wed Dec 2 19:57:52 2020 30%......... (T -0.040 seconds) ETA: Wed Dec 2 19:57:52 2020 40%......... (T -0.034 seconds) ETA: Wed Dec 2 19:57:52 2020 50%......... (T -0.027 seconds) ETA: Wed Dec 2 19:57:52 2020 60%......... (T -0.020 seconds) ETA: Wed Dec 2 19:57:52 2020 70%......... (T -0.014 seconds) ETA: Wed Dec 2 19:57:52 2020 80%......... (T -0.007 seconds) ETA: Wed Dec 2 19:57:52 2020 90%......... Hashing NZ_GG705055.gbk forwards 0%......... (T -0.061 seconds) ETA: Wed Dec 2 19:57:52 2020 10%......... (T -0.056 seconds) ETA: Wed Dec 2 19:57:52 2020 20%......... (T -0.049 seconds) ETA: Wed Dec 2 19:57:52 2020 30%......... (T -0.042 seconds) ETA: Wed Dec 2 19:57:52 2020 40%......... (T -0.035 seconds) ETA: Wed Dec 2 19:57:52 2020 50%......... (T -0.028 seconds) ETA: Wed Dec 2 19:57:52 2020 60%......... (T -0.021 seconds) ETA: Wed Dec 2 19:57:52 2020 70%......... (T -0.014 seconds) ETA: Wed Dec 2 19:57:52 2020 80%......... (T -0.007 seconds) ETA: Wed Dec 2 19:57:52 2020 90%......... Hashing NZ_GG705055.gbk backwards 0%......... (T -0.061 seconds) ETA: Wed Dec 2 19:57:52 2020 10%......... (T -0.055 seconds) ETA: Wed Dec 2 19:57:52 2020 20%......... (T -0.049 seconds) ETA: Wed Dec 2 19:57:52 2020 30%......... (T -0.042 seconds) ETA: Wed Dec 2 19:57:52 2020 40%......... (T -0.035 seconds) ETA: Wed Dec 2 19:57:52 2020 50%......... (T -0.028 seconds) ETA: Wed Dec 2 19:57:52 2020 60%......... (T -0.021 seconds) ETA: Wed Dec 2 19:57:52 2020 70%......... (T -0.014 seconds) ETA: Wed Dec 2 19:57:52 2020 80%......... (T -0.007 seconds) ETA: Wed Dec 2 19:57:52 2020 90%......... Initial hashing took: 0.276 seconds Extracting anchors from hash-space. (T -2.880 seconds) ETA: Wed Dec 2 19:57:55 2020 6%. (T -2.808 seconds) ETA: Wed Dec 2 19:57:56 2020 18%. (T -1.969 seconds) ETA: Wed Dec 2 19:57:55 2020 31%. (T -1.598 seconds) ETA: Wed Dec 2 19:57:55 2020 43%. (T -1.202 seconds) ETA: Wed Dec 2 19:57:55 2020 56%. (T -0.898 seconds) ETA: Wed Dec 2 19:57:55 2020 68%. (T -0.514 seconds) ETA: Wed Dec 2 19:57:55 2020 81%. (T -0.199 seconds) ETA: Wed Dec 2 19:57:55 2020 93%. Anchor extraction completed in: 2.818 seconds Total anchors: 0 Anchor extraction + merge time: 2.818 seconds Total processing time: 3.364 seconds Writing anchors... Total seeds used in anchors: 16 Hash performance: Keys used: 16 out of 16 possible (100.00%). Used keyspace is 100.00% = 100.00% of magic *optimal 100.00% Average pigeons per pigeon hole: 1 Writing 16 repeats...Output writing finished in: 0.485 seconds Total time: 3.849 seconds Murasaki finished! PASSED MURASAKI Testing Genepare on NZ_GG705055.fna 1001 PASSED GENEPARSE Testing mbfa on NZ_GG705055.fna /tmp/autopkgtest-lxc.razmgtoz/downtmp/build.P6A/src/debian/tests/run-unit-test: line 17: 6660 Bus error mbfa $f --fasta > testfile autopkgtest [19:57:56]: test run-unit-test: -----------------------]
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